Feature finding with MZmine2¶
Please follow this (link) to install the software and dependencies.
Complete workflow view¶
complete workflow view
1. Start mzMine2¶
start mzMine
4. Specify intensity cut-off and mass list¶
specify intensity cut-off
5. Build XICs with chromatogram builder¶
Build XICs with chromatogram builder
6. Specify mass list, mass tolerance min. time span and min. hight¶
Specify mass list, mass tolerance min. time span and min. hight
7. Deconvolute isobaric peaks with chromatogram deconvolution¶
Deconvolute isobaric peaks with chromatogram deconvolution
8. Specify algorithm (base line cut-off or local minimum search and parmaters¶
Specify algorithm (base line cut-off or local minimum search and parmaters
9. Perform deisotopization through isotope peak grouper¶
Perform deisotopization through isotope peak grouper
10. Specify parameters for isotope peak grouping¶
Specify parameters for isotope peak grouping
11. Align XICs from different sample to one matrix¶
Align XICs from different sample to one matrix
12. Specify join aligner parameters¶
Specify join aligner parameters
13. [optional] Filter aligned feature matrix with peak list row filter¶
Filter aligned feature matrix with peak list row filter
14. [optional] Depending of your experimental design use n minimum peaks in a row (n should be around the number of replicates or samples you expect to be similar) and 2-3 minimum peaks per isotope pattern¶
use n minimum peaks in a row
15. [optional] You gap filling the re-analyses missed peaks and fill gaps in the feature matrix¶
You gap filling the re-analyses missed peaks and fill gaps in the feature matrix
16. [optional] Depending on experimental design you can normalize your peak intensities to internal standards, TICs or total peak area.¶
normalize your peak intensities to internal standards, TICs or total peak area
17. [optional] Specify normalization parameters¶
Specify normalization parameters
18. Export your matrix as .csv file for down stream data analysis¶
Export your matrix as .csv file for down stream data analysis
19. select file name and parameters you want to export¶
select file name and parameters you want to export
select file name and parameters you want to export
Here is also a video for MZmine 2 documentation: